Yep I agree with where your coming from. Those green things are definately not in that form inside the liver, i'm sure of that. I think the flush does expel bile and this coagulates during the night. The fact that they melt so easily substantiates my belief that they are formed in a six-eight hour period.
Alot of people have claimed to have flushed clean, but I bet if they did the double flush of night and morning oil they would soon start producing stones again, either during that double cleanse or soon after.
It makes certain people lose their stuffy noses in the summer though so it's not doing any harm.
The fact that Andreas Moritz places so much emphasis on the mental side of recovering shows that the stones theory is bogus though. If your emotional disposition was as important as he makes out, you shouldn't have to do the flushes in the first place.